Selective Inhibitors for one of six Ion Channel Isoforms
Mitigating off-target effects within higly similar ion channels family
Background
The family of highly similar ion channel isoforms.
Only oneof which have to be targeted.
The exact location of the most favorable binding pocket for achieving selectivity is unknown.
The goal is to design highly selective inhibitors against 6 ion channel isoforms.
Methodology
Three tentative binding sites were identified for each protein isoform by proprietary Receptor.AI pocket detection workflow:
in the outer channel pore,
inside the channel cavity,
between the functionally important transmembrane helices.
Selectivity assessment based on differential pocket pharmacophore’s representation combined with generative AI binding pose prediction was used.
Pre-filtered stock chemical space of 662K compounds was used as well as custom focused diversity database of50K compounds.
291 compounds were selected for experimental validation.
Results
Three metrics were used:
Fold increase of effect on target isoform in comparison to off-target isoforms.
UFD effect: the preference of the compound to block the active channel state relative to the resting state.
Peak blocking of the target channel at 120 μM of compound relative to vehicle.
The best compound have shown x3.16 selectivity against the target isoform.
Top 5 compounds demonstrate >x2 selectivity and specificity to active state of the target channel, which demonstrates correct mechanism of action against the active channel conformation.
Top 10 compounds are attributed to all three binding pockets.
The top 3 compounds was tested for activity in vivo (murine model) and are proven to be active (including a highly potent one) and non-toxic.